In season three, Pacey agrees to look after Joey Potter as a favor to Dawson as he says that he won't be around to look after Joey.
He buys and restores a wrecked boat, occupying himself with the project to get over Andie, in addition to looking after for Joey.
He gets into a fight with a bully who admits to vandalizing a mural Joey paints for the school.
As the season progresses, Pacey's feelings for Joey begin to deepen. In the episode, "A Weekend in the Country", Pacey comes upon Joey asleep in front of the fire and he sits down to watch her. Conflicted of his feelings for Joey, Pacey continues to be there for her whether it is teaching her how to drive, organizing a student protest, or renting a wall for her next mural. He eventually acts on them and kisses Joey in "Cinderella Story". Despite her concerns about Dawson and Andie's feelings, Joey finally gives into her feelings for Pacey during a weekend away from Capeside in "Stolen Kisses". Pacey and Dawson's friendship is ruined when Dawson learns of Pacey and Joey's relationship in the episode "The Longest Day". A romantic triangle develops between Joey, Pacey, and Dawson.
Joey decides that she needs some space and time to figure out her heart. At the end of the season, Pacey decides to leave Capeside and spend the summer sailing, but not before making one last grand gesture to Joey. Realizing that she is in love with Pacey, Joey races to meet him before he sets sail. Pacey and Joey then leave Capeside for the summer on his boat, the True Love.

In season four, Pacey and Joey return from their summer at sea and still madly in love. They adjust to life back in Capeside as a couple. Pacey continues to struggle with school as he and Joey ponder their futures beyond Capeside. Throughout the majority of the season they re-affirm their commitment to one
another and are chosen "Class Couple". On the senior class ski trip, Pacey and Joey eventually consummate their relationship. Pacey is later hurt to learn that Joey lies to Dawson about this at first, though she eventually tells him the truth.
Towards the end of the season, Pacey and Joey begin having difficulties stemming from the future beyond high school. Believing that he's holding Joey back and growing frustrated with himself and what he sees as his lack of prospects beyond high school, Pacey eventually breaks up with Joey at the senior prom. Despite their strong feelings for each other, both sadly go their separate ways for now. The season ends with Pacey graduating high school and taking a job on a yacht and leaving Capeside once again.

In season six, Pacey finds financial success as a stockbroker in a small stock trading firm in Boston which was set up by Audrey's father. Audrey breaks things off with him as his new job has a dramatic effect on his lifestyle, which clashes with hers. Soon after, Pacey admits that he is not completely over Joey. They share a kiss following a party at Pacey's apartment and in a later episode both are marooned overnight in a K-Mart. Being locked in together overnight, the situation forces the two to discuss their past (and current) relationship, with both admitting that they miss the other. They attempt a reconciliation, but Joey ends things when her recent ex-boyfriend, Eddie, suddenly reappears.

Five years later, a 25-year-old Pacey is now the proprietor of the Ice House, a successful restaurant in Capeside bearing the same name as the one Joey's family used to operate. When everyone returns to Capeside for Gail Leery 's wedding, sparks fly between Pacey and Joey, but their reunion is interrupted when they discover that Jen is dying. The two spend time together in Capeside while Jen is hospitalized. Following Jen's death, they admit that things have kept them apart over the years, but they realize that they're still in love with each other. The series ends with Pacey and Joey romantically together watching the season finale episode of Dawson's television series, The Creek, which is based on their childhood in Capeside.